pypi: HTSeq | Projects | Ecosyste.ms: Papers

10.1016/j.molmet.2018.11.010

Deletion of myeloid IRS2 enhances adipose tissue sympathetic nerve function and limits obesity
Cited by: 16
Author(s): Marie-Therese Rached, Steven Millership, Silvia Pedroni, Agharul I. Choudhury, Ana S.H. Costa, Darran G. Hardy, Justyna Glegola, Elaine E. Irvine, Colin Selman, Megan Woodberry, Vijay K. Yadav, Sanjay Khadayate, António Vidal-Puig, Samuel Virtue, Christian Frezza, Dominic J. Withers
Software Mentions: 2
Published: over 7 years ago

10.1186/s13024-017-0212-x

Hexokinases link DJ-1 to the PINK1/parkin pathway
Cited by: 41
Author(s): David N. Hauser, Adamantios Mamais, Mary Anne Conti, Christopher T. Primiani, R. Ileng Kumaran, Allissa Dillman, Rebekah G. Langston, Alexandra Beilina, Joseph H. Garcia, Alberto Díaz‐Ruiz, Michel Bernier, Fabienne C. Fiesel, Xu Hou, Wolfdieter Springer, Yán Li, Rafael de Cabo, Mark Cookson
Software Mentions: 2
Published: almost 9 years ago

10.1002/1878-0261.12489

Identification of lnc <scp>RNA</scp> s associated with early‐stage breast cancer and their prognostic implications
Cited by: 39
Author(s): Arunagiri Kuha Deva Magendhra Rao, Krishna Patel, Suneetha Korivi Jyothiraj, Balaiah Meenakumari, Shirley Sundersingh, Velusami Sridevi, Thangarajan Rajkumar, Akhilesh Pandey, Aditi Chatterjee, Harsha Gowda, Samson Mani
Software Mentions: 2
Published: over 7 years ago

10.1038/s41380-018-0260-9

SSRIs target prefrontal to raphe circuits during development modulating synaptic connectivity and emotional behavior
Cited by: 52
Author(s): Mariano Soiza-Reilly, Frank J. Meye, Jimmy Olusakin, Ludovic Telley, Emilie Petit, X Chen, Manuel Mameli, Denis Jabaudon, J-Y Sze, Patricia Gaspar
Software Mentions: 2
Published: almost 8 years ago

10.1016/j.ymthe.2018.08.023

Recombinant BCG Overexpressing phoP-phoR Confers Enhanced Protection against Tuberculosis
Cited by: 14
Author(s): Sang Kyun Ahn, Vanessa Tran, Andrea S. Leung, Mark Ng, Ming Li, Jun Liu
Software Mentions: 2
Published: almost 8 years ago

10.1038/s41385-020-00348-5

IL-22 receptor signaling in Paneth cells is critical for their maturation, microbiota colonization, Th17-related immune responses, and anti-Salmonella immunity
Cited by: 33
Author(s): Stephen Gaudino, Michael Beaupre, Xun Lin, Preet Joshi, Sonika Rathi, Patrick A. McLaughlin, Cody Kempen, Neil K. Mehta, Onur Eskiocak, Brian Yueh, Richard S. Blumberg, Adrianus W. M. van der Velden, Kenneth R. Shroyer, Agnieszka B. Bialkowska, Semir Beyaz, Perikala V. Kumar
Software Mentions: 2
Published: over 5 years ago

10.1186/s13567-014-0104-9

Biofilm formation by virulent and non-virulent strains of Haemophilus parasuis
Cited by: 25
Author(s): Bernardo Bello-Ortí, Vincent Deslandes, Yannick D. N. Tremblay, Josée Labrie, Kate J. Howell, Alexander W. Tucker, Duncan J. Maskell, Virginia Aragón, Mario Jacques
Software Mentions: 2
Published: almost 12 years ago

10.1186/s13567-017-0456-z

RNA-seq comparative analysis of Peking ducks spleen gene expression 24 h post-infected with duck plague virulent or attenuated virus
Cited by: 17
Author(s): Lijun Tian, Anchun Cheng, Mingshu Wang, Renyong Jia, Qiao Yang, Ying Wu, Kunfeng Sun, Dekang Zhu, Shun Chen, Mafeng Liu, Xinxin Zhao, Xiaoyue Chen
Software Mentions: 2
Published: about 9 years ago

10.3390/vetsci6020036

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq
Cited by: 6
Author(s): Chandra Shekhar Pareek, Mateusz Sachajko, J. M. Jaśkowski, Magdalena Herudzińska, Mariusz T. Skowroński, Krzysztof Domagalski, Joanna Szczepanek, Urszula Czarnik, P. Sobiech, Dominika Wysocka, Mariusz Pierzchała, Ewa Poławska, Kamila Stepanow, Magdalena Ogłuszka, Edyta Juszczuk-Kubiak, Yaping Feng, Dibyendu Kumar
Software Mentions: 2
Published: over 7 years ago

10.1080/21505594.2018.1514237

Transcription factors Rv0081 and Rv3334 connect the early and the enduring hypoxic response of Mycobacterium tuberculosis
Cited by: 15
Author(s): Xian Sun, Lu Zhang, Jun Jiang, Mark Ng, Zhenling Cui, Juntao Mai, Sang Kyun Ahn, Jingqian Liu, Jinyu Zhang, Jun Liu, Yao Li
Software Mentions: 2
Published: almost 8 years ago

10.1080/21505594.2019.1707957

Determination of antiviral action of long non-coding RNA loc107051710 during infectious bursal disease virus infection due to enhancement of interferon production
Cited by: 15
Author(s): Xing Huang, Yigang Xu, Qingyu Lin, Weilong Guo, Di Zhao, Chunmei Wang, Li Wang, Han Zhou, Yanping Jiang, Wen Cui, Xinyuan Qiao, Guangqiang Ma, Lijie Tang
Software Mentions: 2
Published: over 6 years ago

10.1080/21505594.2021.1936767

YhjC is a novel transcriptional regulator required for Shigella flexneri virulence
Cited by: 7
Author(s): Wanwu Li, Lingyan Jiang, Xiaoqian Liu, Rui Guo, Shuai Ma, Jingting Wang, Shuangshuang Ma, Shujie Li, Huiying Li
Software Mentions: 2
Published: about 5 years ago

10.1080/21505594.2021.1972202

Role of intestinal extracellular matrix-related signaling in porcine epidemic diarrhea virus infection
Cited by: 3
Author(s): Yuchen Li, Jianda Li, Xiuyu Wang, Qingxin Wu, Qian Yang
Software Mentions: 2
Published: about 5 years ago

10.3390/v10040162

Deep Sequencing-Based Transcriptome Profiling Reveals Avian Interferon-Stimulated Genes and Provides Comprehensive Insight into Newcastle Disease Virus-Induced Host Responses
Cited by: 24
Author(s): Weiwei Liu, Xusheng Qiu, Song Chen, Yingjie Sun, Meng Chen, Ying Liao, Lei Tan, Zhuang Ding, Xiufan Liu, Chan Ding
Software Mentions: 2
Published: over 8 years ago

10.3390/v12060620

YerA41, a Yersinia ruckeri Bacteriophage: Determination of a Non-Sequencable DNA Bacteriophage Genome via RNA-Sequencing
Cited by: 7
Author(s): Katarzyna Leskinen, Maria I. Pajunen, Miguel Vincente Gomez-Raya Vilanova, Saija Kiljunen, Andrew Nelson, Darren Smith, Mikael Skurnik
Software Mentions: 2
Published: over 6 years ago

10.3390/v12070713

Long Term Delta-9-tetrahydrocannabinol Administration Inhibits Proinflammatory Responses in Minor Salivary Glands of Chronically Simian Immunodeficieny Virus Infected Rhesus Macaques
Cited by: 7
Author(s): Xavier Álvarez, Karol Sestak, Siddappa N. Byrareddy, Mahesh Mohan
Software Mentions: 2
Published: about 6 years ago

10.1017/pao.2019.1

Effects of diethylcarbamazine and ivermectin treatment onBrugia malayigene expression in infected gerbils (Meriones unguiculatus)
Cited by: 6
Author(s): Morag MacLean, W. Walter Lorenz, Michael T. Dzimianski, Christopher Anna, Andrew R. Moorhead, Barbara J. Reaves, Adrian J. Wolstenholme
Software Mentions: 2
Published: over 7 years ago

10.1186/s13071-017-1990-2

Transcriptomic responses of water buffalo liver to infection with the digenetic fluke Fasciola gigantica
Cited by: 23
Author(s): Fu-Kai Zhang, Xiaoxuan Zhang, Hany M. Elsheikha, Jun-Jun He, Zhao-An Sheng, Wei Zheng, Jian-Gang Ma, Weiyi Huang, Aijiang Guo, Xingquan Zhu
Software Mentions: 2
Published: over 9 years ago

10.1186/s13071-018-3179-8

Transcriptomic insights into the early host-pathogen interaction of cat intestine with Toxoplasma gondii
Cited by: 8
Author(s): Meng Wang, Fu-Kai Zhang, Hany M. Elsheikha, Nian‐Zhang Zhang, Jun-Jun He, Jianxun Luo, Xingquan Zhu
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12969-019-0347-0

Plasma exosomes from children with juvenile dermatomyositis are taken up by human aortic endothelial cells and are associated with altered gene expression in those cells
Cited by: 10
Author(s): Kaiyu Jiang, Rie Karasawa, Zihua Hu, Yanmin Chen, Lucy C Holmes, Kathleen M. O’Neil, James N. Jarvis
Software Mentions: 2
Published: about 7 years ago

10.7717/peerj.11714

Short-term high fat diet alters genes associated with metabolic and vascular dysfunction during adolescence in rats: a pilot study
Cited by: 1
Author(s): Alex E. Mohr, Rebecca A. Reiss, Monique Beaudet, Johnny A. Sena, Jay S. Naik, Benjimen R. Walker, Karen L. Sweazea
Software Mentions: 2
Published: about 5 years ago

10.7717/peerj.8684

Comprehensive phenotyping and transcriptome profiling to study nanotoxicity inC. elegans
Cited by: 10
Author(s): Charles Viau, Orçun Haçarız, Farial Karimian, Jianguo Xia
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.869

Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols
Cited by: 24
Author(s): Peter A. Combs, Michael B. Eisen
Software Mentions: 2
Published: over 11 years ago

10.7717/peerj.2620

Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses
Cited by: 29
Author(s): Zhuo Huang, Si-Han Jin, Han-Du Guo, Xiao‐bo Zhong, Junlin He, Xi Li, Mingyan Jiang, Xiaofang Yu, Hai Long, Min Ma, Qibing Chen
Software Mentions: 2
Published: almost 10 years ago

10.7717/peerj.2664

Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content inLarimichthys crocea
Cited by: 18
Author(s): Shijun Xiao, Panpan Wang, Linsong Dong, Yaguang Zhang, Zhaofang Han, Qiurong Wang, Zhiyong Wang
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.10500

Transcriptional profile in rat muscle: down-regulation networks in acute strenuous exercise
Cited by: 1
Author(s): Stela Mirla da Silva Felipe, Raquel Martins de Freitas, Emanuel Diego dos Santos Penha, Christina Pacheco, Daniel Freitas Freire Martins, Juliana Osório Alves, Paula Matias Soares, Adriano César Carneiro Loureiro, Tanes I. Lima, Leonardo R. Silveira, Alex Soares Marreiros Ferraz, Jorge Estefano Santana de Souza, José Henrique Leal-Cardoso, Denise Pires de Carvalho, Vânia Marilande Ceccatto
Software Mentions: 2
Published: over 5 years ago

10.7717/peerj.5103

Transcriptomic evidence for involvement of reactive oxygen species in Rhizoctonia solani AG1 IA sclerotia maturation
Cited by: 9
Author(s): Bo Liu, Haode Wang, Zhoujie Ma, Xiaotong Gai, Yanqiu Sun, Shidao He, Xian Liu, Yanfeng Wang, Yue Xuan, Zhen Gao
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.2945

Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
Cited by: 71
Author(s): William J. Brazelton, Christopher N Thornton, Alex Hyer, Katrina I. Twing, August Longino, Susan Q. Lang, Marvin D. Lilley, Gretchen L. Früh-Green, M. O. Schrenk
Software Mentions: 2
Published: over 9 years ago

10.7717/peerj.1762

Epithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues
Cited by: 46
Author(s): Ruidong Xiang, V. H. Oddy, Alan Archibald, Phil Vercoe, Brian P. Dalrymple
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.9172

Transcriptome profiling of avian pathogenicEscherichia coliand the mouse microvascular endothelial cell line bEnd.3 during interaction
Cited by: 6
Author(s): Peili Wang, Xianli Meng, Jianji Li, Yanfei Chen, Dong Zhang, Haoran Zhong, Pengpeng Xia, Luying Cui, Guoqiang Zhu, Heng Wang
Software Mentions: 2
Published: over 6 years ago

10.7717/peerj.1991

Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew
Cited by: 17
Author(s): Yanping Li, Shilin Tian, Xiaojun Yang, Xin Wang, Yuhai Guo, Hanwen Ni
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.4537

Flavonoid biosynthesis controls fiber color in naturally colored cotton
Cited by: 20
Author(s): Haifeng Liu, Cheng Luo, Song Wu, Haitao Shen, Guoliang Li, Zhigang He, Wen-Gang Chen, Yanyan Cao, Fang Huang, Shouwu Tang, Hong Pan, Enfeng Zhao, Jianbo Zhu, Dajun He, Shaoming Wang, Guang-Ying Huo, Hailiang Liu
Software Mentions: 2
Published: over 8 years ago

10.7717/peerj.3945

Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C
Cited by: 63
Author(s): Alexey Gilman, Yanfen Fu, Melissa C. Hendershott, Frances Chu, Aaron W. Puri, Amanda Lee Smith, Mitchell W. Pesesky, Rose Lieberman, David A. C. Beck, Mary E. Lidstrom
Software Mentions: 2
Published: almost 9 years ago

10.14814/phy2.12450

Unique gene program of rat small resistance mesenteric arteries as revealed by deep RNA sequencing
Cited by: 8
Author(s): John J Reho, Amol C. Shetty, Rachael P. Dippold, Anup Mahurkar, Steven A. Fisher
Software Mentions: 2
Published: about 11 years ago

10.14814/phy2.12481

Perilipin 4 in human skeletal muscle: localization and effect of physical activity
Cited by: 37
Author(s): Shirin Pourteymour, Sindre Lee, Torgrim M. Langleite, Kristin Eckardt, Marit Hjorth, Christian Bindesbøll, Knut Tomas Dalen, Kåre I. Birkeland, Christian A. Drevon, Torgeir Holen, Frode Norheim
Software Mentions: 2
Published: about 11 years ago

10.14814/phy2.12109

Regulation of angiopoietin-like protein 4 production during and after exercise
Cited by: 35
Author(s): Frode Norheim, Marit Hjorth, Torgrim M. Langleite, Sindre Lee, Torgeir Holen, Christian Bindesbøll, Hans Kristian Stadheim, Hanne Løvdal Gulseth, Kåre I. Birkeland, Anders Kielland, Jørgen Jensen, Knut Tomas Dalen, Christian A. Drevon
Software Mentions: 2
Published: about 12 years ago

10.1111/pbi.13310

Deciphering the high‐quality genome sequence of coriander that causes controversial feelings
Cited by: 51
Author(s): Xiaoming Song, Jinpeng Wang, Nan Li, Jigao Yu, Fanbo Meng, Chendan Wei, Chao Liu, Wei Chen, Fulei Nie, Zhikang Zhang, Ke Gong, Xinyu Li, Jingjing Hu, Qing Yang, Yuxian Li, Chunjin Li, Shuyan Feng, He Guo, Jiaqing Yuan, Qiaoying Pei, Tong Yu, Xi Kang, Wei Zhao, Tianyu Lei, Pengchuan Sun, Li Wang, Weina Ge, Di Guo, Xiaoyang Duan, Shaoqi Shen, Chunlin Cui, Ying Yu, Yangqin Xie, Zhang Jin, Yayi Hou, Jinyu Wang, Xiuqing Li, Andrew H. Paterson, Xiyin Wang
Software Mentions: 2
Published: over 6 years ago

10.1111/pbi.12820

Single‐base methylome analysis reveals dynamic epigenomic differences associated with water deficit in apple
Cited by: 123
Author(s): Jidi Xu, Shasha Zhou, Xiaoqing Gong, Yi Song, Steve van Nocker, Fengwang Ma, Qingmei Guan
Software Mentions: 2
Published: almost 9 years ago

10.1111/pbi.13044

Genes regulating gland development in the cotton plant
Cited by: 39
Author(s): Madhusudhana R. Janga, Devendra Pandeya, LeAnne M. Campbell, Kranti Konganti, Stephany Toinga Villafuerte, Lorraine S. Puckhaber, Alan E. Pepper, Robert D. Stipanovic, Jodi A. Scheffler, Keerti S. Rathore
Software Mentions: 2
Published: over 7 years ago

10.1111/pbi.12548

Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off‐target pathways through metabolite signalling
Cited by: 26
Author(s): Elise K. Pasoreck, Jin Su, Ian M. Silverman, Sager J. Gosai, Brian D. Gregory, Joshua S. Yuan, Henry Daniell
Software Mentions: 2
Published: over 10 years ago

10.1002/pld3.15

Diverse contributions of MYC2 and EIN3 in the regulation of Arabidopsis jasmonate-responsive gene expression
Cited by: 7
Author(s): Yuyu Zheng, Yiheng Lan, Tieliu Shi, Ziqiang Zhu
Software Mentions: 2
Published: almost 9 years ago

10.1002/pld3.292

Cytokinin isopentenyladenine and its glucoside isopentenyladenine‐9G delay leaf senescence through activation of cytokinin‐associated genes
Cited by: 10
Author(s): H Tucker Hallmark, Aaron M. Rashotte
Software Mentions: 2
Published: almost 6 years ago

10.1002/pld3.48

Ethylene causes transcriptomic changes in Synechocystis during phototaxis
Cited by: 11
Author(s): Randy F. Lacey, Cidney J. Allen, Arkadipta Bakshi, Brad M. Binder
Software Mentions: 2
Published: over 8 years ago

10.3390/plants9111507

Search for New Allergens in Lolium perenne Pollen Growing under Different Air Pollution Conditions by Comparative Transcriptome Study
Cited by: 0
Author(s): Jose Antonio Lucas, Enrique Gutierrez‐Albanchez, Teresa Alfaya, Francisco Feo Brito, Francisco Javier Gutiérrez-Mañero
Software Mentions: 2
Published: almost 6 years ago

10.3390/plants9101308

Transcriptome Analyses and Antioxidant Activity Profiling Reveal the Role of a Lignin-Derived Biostimulant Seed Treatment in Enhancing Heat Stress Tolerance in Soybean
Cited by: 35
Author(s): Cristina Campobenedetto, Giuseppe Mannino, Chiara Agliassa, Alberto Acquadro, Valeria Contartese, Christian Garabello, Cinzia M. Bertea
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pbio.2005594

The mammalian decidual cell evolved from a cellular stress response
Cited by: 75
Author(s): Eric M. Erkenbrack, Jamie Maziarz, Oliver W. Griffith, Cong Liang, Arun R. Chavan, Mauris C. Nnamani, Günter P. Wagner
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pbio.2006716

miR-181a/b-1 controls thymic selection of Treg cells and tunes their suppressive capacity
Cited by: 26
Author(s): Marcin Łyszkiewicz, Samantha J Winter, Katrin Witzlau, Lisa Föhse, Rebecca J. Brownlie, Jacek Puchałka, Nikita A. Verheyden, Heike Kunze‐Schumacher, Esther Imelmann, Jonas Blume, Solaiman Raha, Takashi Sekiya, Akihiko Yoshimura, Jochen T. Frueh, Evelyn Ullrich, Jochen Huehn, Siegfried Weiß, Maximiliano G. Gutiérrez, Immo Prinz, Rose Zamoyska, Natalia Ziętara, Andreas Krueger
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pcbi.1005457

Transcriptomics technologies
Cited by: 589
Author(s): Russell Lowe, Neil J. Shirley, Mark R. Bleackley, Stephen K. Dolan, Thomas Shafee
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pcbi.1005629

Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype
Cited by: 57
Author(s): Eilon Sharon, Sancun Hao, Sandhya Kharbanda, Winston Koh, Lance Martin, Kiran K. Khush, Hannah A. Valantine, Jonathan K. Pritchard, Iwijn De Vlaminck
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pcbi.1008006

Epigenome-based splicing prediction using a recurrent neural network
Cited by: 15
Author(s): Dong‐Hoon Lee, Jing Zhang, Jason Liu, Mark Gerstein
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pcbi.1005895

Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting
Cited by: 24
Author(s): Alyaa M. Abdel-Haleem, Hooman Hefzi, Katsuhiko Mineta, Xin Gao, Takashi Gojobori, Jaehyung Kim, Nathan E. Lewis, Neema Jamshidi
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1005588

Modulation of Ambient Temperature-Dependent Flowering in Arabidopsis thaliana by Natural Variation of FLOWERING LOCUS M
Cited by: 78
Author(s): Ulrich Lutz, David Posé, Matthias Pfeifer, Heidrun Gundlach, Jörg Hagmann, Congmao Wang, Detlef Weigel, Klaus Mayer, Markus Schmid, Claus Schwechheimer
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pgen.1006737

A fungal transcription factor essential for starch degradation affects integration of carbon and nitrogen metabolism
Cited by: 41
Author(s): Yi Xiong, V. Wu, Andrea Lubbe, Lu‐Ping Qin, Shijie Deng, Megan Kennedy, Diane Bauer, Vasanth Singan, Kerrie Barry, Trent Northen, Igor V. Grigoriev, N. Louise Glass
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pgen.1003569

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs
Cited by: 626
Author(s): Matthew J. Hangauer, Ian W. Vaughn, Michael T. McManus
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pgen.1007292

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements
Cited by: 20
Author(s): Timothy L. Haskett, Jason Terpolilli, Vinoy K. Ramachandran, Callum J. Verdonk, Phillip Poole, G.W. O’Hara, Joshua P. Ramsay
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pgen.1006129

Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome
Cited by: 43
Author(s): Ronghui Li, Qiaoxiang Dong, Xinni Yuan, Xin Zeng, Yu Gao, Cassandra Chiao, Hongda Li, Xinyu Zhao, Sündüz Keleş, Zefeng Wang, Qiang Chang
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0229892

All-trans retinoic acid induces reprogramming of canine dedifferentiated cells into neuron-like cells
Cited by: 9
Author(s): Rei Nakano, Taku Kitanaka, Shinichi Namba, Nanako Kitanaka, Masaki Sato, Yoshiyuki Shibukawa, Yoshikazu Masuhiro, Koichiro Kano, Tarô Matsumoto, Hiroshi Saito
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0246818

Transcriptome analyses reveal the utilization of nitrogen sources and related metabolic mechanisms of Sporosarcina pasteurii
Cited by: 7
Author(s): Di Pei, Zhiming Liu, Wenjian Wu, Biru Hu
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0152540

Gene Expression Profile in the Long-Living Lotus: Insights into the Heat Stress Response Mechanism
Cited by: 6
Author(s): Xiaojing Liu, Fengfeng Du, Naiwei Li, Yajun Chang, Dongrui Yao
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0233789

Sevoflurane depletes macrophages from the melanoma microenvironment
Cited by: 7
Author(s): Isabella Sztwiertnia, Judith Schenz, Katharina Bomans, Dominik Schaack, Johanna Ohnesorge, Sandra Tamulyte, Markus Weigand, Florian Uhle
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0116125

The Kidney Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling
Cited by: 46
Author(s): Masato Habuka, Linn Fagerberg, Björn M. Hallström, Caroline Kampf, Karolina Edlund, Åsa Sivertsson, Tadashi Yamamoto, Fredrik Pontén, Mathias Uhlén, Jacob Odeberg
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0206379

De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish
Cited by: 12
Author(s): Luciana Watanabe, Fátima Gomes, João L.S.G. Vianez, Márcio Roberto Teixeira Nunes, Jedson Ferreira Cardoso, Clayton Pereira da Silva de Lima, Horácio Schneider, Iracilda Sampaio
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0219163

Transcriptional profiling of Salmonella enterica serovar Enteritidis exposed to ethanolic extract of organic cranberry pomace
Cited by: 23
Author(s): Quail Das, Dion Lepp, Yin X, Kelly Ross, Jason McCallum, Keith Warriner, Massimo F. Marcone, Moussa S. Diarra
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0120691

Comparative Transcriptome Profiling of the Early Infection of Wheat Roots by Gaeumannomyces graminis var. tritici
Cited by: 18
Author(s): Lirong Yang, Lin Xie, Xue Bao-guo, Paul H. Goodwin, Xin Quan, Chuanlin Zheng, Taiguo Liu, Zhensheng Lei, Xiaohong Yang, Yue-en Chao, Chao Wu
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0100883

A GPBAR1 (TGR5) Small Molecule Agonist Shows Specific Inhibitory Effects on Myeloid Cell Activation In Vitro and Reduces Experimental Autoimmune Encephalitis (EAE) In Vivo
Cited by: 51
Author(s): Nuruddeen D. Lewis, Lori Patnaude, Josephine Pelletier, Donald Souza, Susan Lukas, Jim King, Jonathan D. Hill, Dimitria E. Stefanopoulos, Kelli R. Ryan, Sudha Desai, Donna Skow, Stefan G. Kauschke, Andre Broermann, Daniel Kuzmich, Christian Harcken, Eugene R. Hickey, Louise K. Modis
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0201628

Transcriptional profiling of two different physiological states of the yak mammary gland using RNA sequencing
Cited by: 7
Author(s): Jinjiang Fan, Yuzhu Luo, Sijiu Yu, Yan Cui, Gezhi Xu, Libin Wang, Yangyang Pan, Honghong He
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0208526

Transcriptome-wide analysis links the short-term expression of the b isoforms of TIA proteins to protective proteostasis-mediated cell quiescence response
Cited by: 7
Author(s): Isabel Carrascoso, José Alcalde, Daniel Tabas-Madrid, Juan Carlos Oliveros, José M. Izquierdo
Software Mentions: 2
Published: almost 8 years ago

10.1371/journal.pone.0182568

Genome-wide identification of autosomal genes with allelic imbalance of chromatin state
Cited by: 7
Author(s): Andrej J. Savol, Peggy I. Wang, Yongho Jeon, David Colognori, E. Yildirim, Stefan F. Pinter, Bernhard Payer, Jeannie T. Lee, Ruslan I. Sadreyev
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0130028

Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex
Cited by: 43
Author(s): Evelina Sjöstedt, Linn Fagerberg, Björn M. Hallström, Anna Häggmark, Nicholas Mitsios, Peter Nilsson, Fredrik Pontén, Tomas Hökfelt, Mathias Uhlén, Jan Mulder
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0216082

The protein elicitor Hrip1 enhances resistance to insects and early bolting and flowering in Arabidopsis thaliana
Cited by: 6
Author(s): Xin-yue Miao, Hong-pan Qu, Ya-lei Han, Congfen He, Dewen Qiu, Zhiwei Cheng
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0180925

2-aminoimidazoles potentiate ß-lactam antimicrobial activity against Mycobacterium tuberculosis by reducing ß-lactamase secretion and increasing cell envelope permeability
Cited by: 17
Author(s): Albert B. Jeon, Andrés Obregón-Henao, David F. Ackart, Brendan K. Podell, Juán Manuel Belardinelli, Mary Jackson, Tuan Vu Nguyen, Meghan S. Blackledge, Roberta J. Melander, Benjamin K. Johnson, Robert B. Abramovitch, Randall J. Basaraba
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0179033

Candidate genes on murine chromosome 8 are associated with susceptibility to Staphylococcus aureus infection in mice and are involved with Staphylococcus aureus septicemia in humans
Cited by: 5
Author(s): Qin Yan, Sun Hee Ahn, Felix Mba Medie, Batu K. Sharma-Kuinkel, Lawrence P. Park, William K. Scott, Hitesh Deshmukh, Ephraim L. Tsalik, Derek D. Cyr, Christopher W. Woods, Chen-Hsin Albert Yu, Carlton Adams, Robert Qi, Brenda Hansen, Vance G. Fowler
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0136103

Impaired Cell Cycle Regulation in a Natural Equine Model of Asthma
Cited by: 22
Author(s): Alicja Pacholewska, Vidhya Jagannathan, Michaela Drögemüller, Jolanta Klukowska‐Rötzler, Simone Lanz, Eman Hamza, Emmanouil T. Dermitzakis, Eliane Marti, Tosso Leeb, Vinzenz Gerber
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0216586

Aberrant gene expression by Sertoli cells in infertile men with Sertoli cell-only syndrome
Cited by: 20
Author(s): Darius A. Paduch, Stephanie Hilz, Andrew Grimson, Peter N. Schlegel, Anne Jedlicka, William W. Wright
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0217096

Similar effects of high-fructose and high-glucose feeding in a Drosophila model of obesity and diabetes
Cited by: 29
Author(s): Laura Palanker Musselman, Jill L. Fink, Thomas J. Baranski
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0178923

Comparative transcriptomics of genetically divergent lines of chickens in response to Marek’s disease virus challenge at cytolytic phase
Cited by: 4
Author(s): Kunzhe Dong, Shuang Chang, Qingmei Xie, Alexis Black-Pyrkosz, Huanmin Zhang
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0170961

MicroRNA and mRNA Transcriptome Profiling in Primary Human Astrocytes Infected with Borrelia burgdorferi
Cited by: 21
Author(s): Timothy Casselli, Humaira Qureshi, Elizabeth Peterson, Danielle Perley, Emily J. Blake, Bradley Jokinen, Ata Abbas, Sergei Nechaev, John A. Watt, Archana Dhasarathy, Catherine A. Brissette
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0237699

Analysis of miRNAs and their target genes associated with mucosal damage caused by transport stress in the mallard duck intestine
Cited by: 2
Author(s): Hao Zhang, Fang Chen, Zhen-Hua Liang, Yan Wu, Jinsong Pi, Lixia Wang, Junzheng Du, Jie Shen, Angelo Pan, Yuejin Pu
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pone.0132176

Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.)
Cited by: 30
Author(s): Vasudevan Ayyappan, Venu Kalavacharla, Jyothi Thimmapuram, Ketaki P. Bhide, Venkateswara R. Sripathi, Tomasz G. Smolinski, Muthusamy Manoharan, Yaqoob Thurston, Antonette Todd, Brewster F. Kingham
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0185732

Transcriptome analysis of genes involved in defense against alkaline stress in roots of wild jujube (Ziziphus acidojujuba)
Cited by: 27
Author(s): Mingxin Guo, Shipeng Li, Shan Tian, Bei Wang, Xiangshan Zhao
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0197973

Loss of Fnip1 alters kidney developmental transcriptional program and synergizes with TSC1 loss to promote mTORC1 activation and renal cyst formation
Cited by: 17
Author(s): Ryan Michael Centini, Mark Tsang, Terri Iwata, Heon Park, Jeffrey J. Delrow, Daciana Margineantu, Brian M. Iritani, Haiwei Gu, H. Denny Liggitt, Janella Kang, Lim Kang, David M. Hockenbery, Daniel Raftery
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0091353

Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa
Cited by: 41
Author(s): Yamini Arthanari, Christian Heintzen, Sam Griffiths-Jones, Susan K. Crosthwaite
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0098578

Digital Gene-Expression Profiling Analysis of the Cholesterol-Lowering Effects of Alfalfa Saponin Extract on Laying Hens
Cited by: 14
Author(s): Lu Zhou, Shi Ya, Rui Guo, Minggen Liang, Xiaoyan Zhu, Chengzhang Wang
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0156453

Comprehensive RNA-Seq Analysis on the Regulation of Tomato Ripening by Exogenous Auxin
Cited by: 41
Author(s): Jiayin Li, Xiaoya Tao, Li Li, Linchun Mao, Zisheng Luo, Zia Ullah Khan, Tiejin Ying
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0116309

Gene Expression Dosage Regulation in an Allopolyploid Fish
Cited by: 14
Author(s): Isa Matos, Miguel P. Machado, Manfred Schartl, M. M. Coelho
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0215472

UV-C treatment promotes quality of early ripening apple fruit by regulating malate metabolizing genes during postharvest storage
Cited by: 19
Author(s): Jakaria Chowdhury Onik, Yajing Xie, Yuquan Duan, Xiaojia Hu, Zhidong Wang, Qiong Lin
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0244648

Transcriptomic analysis of the honey bee (Apis mellifera) queen spermathecae reveals genes that may be involved in sperm storage after mating
Cited by: 11
Author(s): Juliana Rangel, Tonya F. Shepherd, Alejandra González, Andrew Hillhouse, Kranti Konganti, Nancy H. Ing
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0184974

Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2
Cited by: 10
Author(s): Yadong Mei, Huan Liu, Shunxi Zhang, Ming Yang, Chun Hu, Jian Zhang, Ping Shen, Xiangdong Chen
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0128350

Putative Regulatory Factors Associated with Intramuscular Fat Content
Cited by: 66
Author(s): A. S. M. César, Luciana Correia de Almeida Regitano, James E. Koltes, Eric R. Fritz-Waters, Dante Pazzanese Duarte Lanna, G. Gasparin, Gerson Barreto Mourão, P. S. N. Oliveira, James M. Reecy, Luiz Lehmann Coutinho
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0179922

Transcriptomic analysis to uncover genes affecting cold resistance in the Chinese honey bee (Apis cerana cerana)
Cited by: 21
Author(s): Kai Xu, Qingsheng Niu, Huiting Zhao, Yali Du, Yusuo Jiang
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0179762

Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes
Cited by: 20
Author(s): Konstantinos Loupasakis, David Kuo, Upneet K. Sokhi, Cheol Ho Sohn, Bethany Syracuse, Ευγενία Γιαννοπούλου, Sung Ho Park, Hee‐Ju Kang, Gunnar Rätsch, Lionel B. Ivashkiv, George D. Kalliolias
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0156045

Transcriptome Analysis and Gene Identification in the Pulmonary Artery of Broilers with Ascites Syndrome
Cited by: 21
Author(s): Fei Yang, Cao H, Qingyang Xiao, Xiaomin Guo, Zhuang Yu, Caiying Zhang, Tiancheng Wang, Huayuan Lin, Yan-Chun Song, Guoliang Hu, Ping Liu
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0217343

Identification of two molecular subtypes in canine mast cell tumours through gene expression profiling
Cited by: 6
Author(s): Lidia Hildebrand Pulz, Camila Neri Barra, Pâmela Almeida Alexandre, Greice Cestari Huete, Karine Germano Cadrobbi, Adriana Tomoko Nishiya, Sílvio Henrique de Freitas, Heidge Fukumasu, Ricardo de Francisco Strefezzi
Software Mentions: 2
Published: about 7 years ago

10.1371/journal.pone.0241966

Transcripts of wheat at a target locus on chromosome 6B associated with increased yield, leaf mass and chlorophyll index under combined drought and heat stress
Cited by: 3
Author(s): Jessica Schmidt, Melissa Garcia, Chris Brien, Priyanka Kalambettu, Trevor Garnett, Delphine Fleury, Penny J. Tricker
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0165953

Genome-Wide Identification, Characterization, and Stress-Responsive Expression Profiling of Genes Encoding LEA (Late Embryogenesis Abundant) Proteins in Moso Bamboo (Phyllostachys edulis)
Cited by: 32
Author(s): Zhuo Huang, Xiaojuan Zhong, Jun He, Si-Han Jin, Han-Du Guo, Xiaofang Yu, Yujue Zhou, Xi Li, Min Ma, Qibing Chen, Hai Long
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0143378

Transcriptional Profiling Identifies Location-Specific and Breed-Specific Differentially Expressed Genes in Embryonic Myogenesis in Anas Platyrhynchos
Cited by: 9
Author(s): Rongping Zhang, Hehe Liu, Junying Liu, Jiwei Hu, Xiping Yan, Ding-min-cheng Wang, Liang Li, Jiwen Wang
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0160970

Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination
Cited by: 17
Author(s): Iana H. Haralambieva, Michael T. Zimmermann, Inna G. Ovsyannikova, Diane E. Grill, Ann L. Oberg, Richard B. Kennedy, Gregory A. Poland
Software Mentions: 2
Published: about 10 years ago

10.1016/j.stem.2020.10.018

Membrane Tension Gates ERK-Mediated Regulation of Pluripotent Cell Fate
Cited by: 94
Author(s): Henry De Belly, Aki Stubb, Akira Yanagida, Céline Labouesse, Philip H. Jones, Ewa K. Paluch, Kevin J. Chalut
Software Mentions: 2
Published: over 5 years ago

10.3390/cells8020112

Suppression of IgE-Independent Degranulation of Murine Connective Tissue-Type Mast Cells by Dexamethasone
Cited by: 10
Author(s): Keiko Yamada, Hitomi Sato, Kazuma Sakamaki, Mayumi Kamada, Yasushi Okuno, Nobuyuki Fukuishi, Kazuyuki Furuta, Satoshi Tanaka
Software Mentions: 2
Published: over 7 years ago

10.3390/cells10092403

Analysis of the Reversible Impact of the Chemodrug Busulfan on Mouse Testes
Cited by: 5
Author(s): Laura Thirouard, Hélène Holota, Mélusine Monrose, Manon Garcia, Angélique De Haze, Jean-Paul Saru, Françoise Caira, Claude Beaudoin, David H. Volle
Software Mentions: 2
Published: about 5 years ago

Projects: pypi: HTSeq

Science Score: 65/100

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Papers Mentioning HTSeq 3,071